Nanosecond-scale ab initio molecular dynamics of fully solvated biomolecules with periodic boundary conditions using the Oak Ridge Leadership Computing Facility (OLCF) supercomputers

We present nanosecond-scale molecular dynamics simulations of small ribonucleic acids with full solvation shells of explicit water and ions at the density functional theory (DFT) level, using high performance ab initio molecular dynamics programs and the Oak Ridge Leadership Computing Facility (OLCF) supercomputers. Comparison of the trajectories to classical molecular dynamics is performed, including effects of polarization, changes in molecular conformations, and dynamics of the system in metastable states and with respect to barrier crossing. We find important differences in the conformational dynamics and analyze the effects of dynamic changes in charge density and polarization that are available from the first-principles description and which may be essential to correct simulation of conformational ensembles of these difficult-to-model molecules.